How? They later changed Ganondorf's design in TP. It was art for TP and TP only. I don't see how "forgetting about it" has anything to do with this. Especially since Ganny wouldn't have fit in SS.
That concept art doesn't really fit for me as a suitable boss to replace Demise in Skyward Sword or bosses for the matter. It works better in a Zelda game where Ganondorf was old and dying, perhaps drained of his power and he intends to find a way to make himself young again much like the Joker from Arkham City. If I have to change the boss design for Demise, I'll give him some kind of battle armor that resembles Demise in the cave paintings, with three horns sticking out and shrouded in shadows.
I like Ghirahim for boss. Ganon's a good idea but not the best.